I just built the SVN version (after many failed attempts to check it out, "connection reset by peer") and the debugger is broken. Whenever you pause (using the >\|| button, breakpoints, etc) it automatically steps through the code as if you were continuously clicking Next. (It does look neat though.

Maybe adding a way to step through a specified number of instructions or step to the next breakpoint like this would be useful.)
The problem seems to be that this (debugger/debugger.c:91) isn't doing anything:
Code:
// Emulation thread is blocked until a button is clicked.
SDL_CondWait(debugger_done_cond, mutex);
Also, I found a way to crash the old version I'd been using by accessing invalid memory addresses, but with the debugger not working I'm not able to test it on this build.
[edit] All I've managed to find is that pthread_cond_wait() is failing. SDL doesn't tell why. SDL_CreateCond() is working.
[edit again] I replaced the SDL_CondWait() with just setting rompause=1. It works on the title screen of Mario 64, but when the Mario head appears, it doesn't pause even though this flag is set. The pause button on the main window magically continues to work, but I see the "Mupen64Plus Started" text above the "Paused" text once the Mario head appears.
[more edit] Well I got that working by adding some more checks for rompause, then I accidentally hit a random key while trying to take this screenshot, and it proceeded to go into an endless loop complaining of SIGSEGV errors and popping up error messages until my X server locked up. >8^( (But I got it back under control by killing the process from SSH. Yay Linux!) I also reimplemented my fix for the buffer overflow in the FPU register display. (Those numbers get up to like 509 digits!) However SVN won't make a patch because "Directory 'mupen64_audio' is missing".
Unfortunately, there's another bug. See if you can figure out what's missing from this image.
[hey more editing] Yeah, if the core thread gets a SIGSEGV, it pops up message boxes in an infinite loop until the system locks up. V_v